In 2003 and 2004, as Pixar's contract with Disney was running out, Jobs and Disney chief executive Michael Eisner tried but failed to negotiate a new partnership, and in January 2004, Jobs announced that he would never deal with Disney again. Pixar would seek a new partner to distribute its films after its contract expired.

In October 2005, Bob Iger replaced Eisner at Disney, and Iger quickly worked to mend relations with Jobs and Pixar. On January 24, 2006, Jobs and Iger announced that Disney had agreed to purchase Pixar in an all-stock transaction worth $7.4 billion. When the deal closed, Jobs became The Walt Disney Company's largest single shareholder with approximately seven percent of the company's stock. Jobs's holdings in Disney far exceeded those of Eisner, who holds 1.7%, and of Disney family member Roy E. Disney, who until his 2009 death held about 1% of the company's stock and whose criticisms of Eisner—especially that he soured Disney's relationship with Pixar—accelerated Eisner's ousting. Upon completion of the merger, Jobs received 7% of Disney shares, and joined the board of directors as the largest individual shareholder. Upon Jobs's death his shares in Disney were transferred to the Steven P. Jobs Trust led by Laurene Jobs.